A new analysis of DNA from more than 3,000 people across Japan has produced some of the most detailed genetic findings about Japanese origins to date. The study challenges a long-held two-ancestry model and uncovers connections between ancient inherited DNA and modern diseases.
Published in Science Advances, the study was led by Xiaoxi Liu of the RIKEN Center for Integrative Medical Sciences in Yokohama, Japan.
Researchers built a dataset called JEWEL by sequencing the full genomes of 3,256 individuals from seven geographic regions, including the main islands and Okinawa.
Using rare genetic variants, which tend to reflect more recent population history, the team identified three distinct ancestral components rather than the two that earlier studies had described. One component was strongest in Okinawa, a second in the northeastern region, and a third in western Japan.
Japanese DNA reveals three distinct population origins
Western Japanese showed the closest genetic ties to Han Chinese. Northeastern Japanese appeared more closely related to ancient Korean populations from the Three Kingdoms period and to the Jomon, Japan’s earliest known inhabitants.
Researchers said these patterns support a “tripartite origins” model that goes beyond the traditional framework.
The ancestry findings also helped explain the geographic spread of two hereditary breast cancer mutations common in Japan. The BRCA1 mutation appeared mostly in people with northeastern ancestry. The BRCA2 mutation was concentrated in those with Western ancestry, suggesting separate continental origins for each.
The dataset revealed 18,481 loss-of-function variants across 9,045 genes. Nearly 9,800 of these had not been recorded in major genetic databases before. Researchers identified one patient carrying two faulty copies of the ABCC2 gene, consistent with Dubin-Johnson syndrome, a liver condition that causes chronic jaundice.
Six individuals carried loss-of-function variants in the PTPRD gene, and three of them shared clinical conditions, including heart attack, kidney failure, and hypertension.
Neanderthal and Denisovan segments tied to diabetes risk
The study also identified 44 genetic segments inherited from Neanderthals and Denisovans. A Denisovan-derived segment near the NKX6-1 gene was linked to type 2 diabetes.
A Neanderthal-derived segment near GLP1R, a gene targeted by diabetes drugs including semaglutide, was also associated with type 2 diabetes.
That segment is present in East Asians but absent in Europeans. Researchers said this difference could affect how certain treatments perform across populations.
The team found strong evidence of recent natural selection in genes tied to alcohol metabolism and immune function, specifically the ADH cluster, ALDH2, and the major histocompatibility complex. These signals were somewhat weaker in Okinawa, which researchers said may warrant further study.
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